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sc-PDB

An Annotated Database of Druggable Binding Sites from the Protein DataBank

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Protein Data Bank Entry:

4kq1

2.660 Å

X-ray

2013-05-14

Interactomes:
Molecular Function:
Binding Site :

Uniprot Annotation

Name:Glycogen [starch] synthase
ID:E7NKU1_YEASO
AC:E7NKU1
Organism:Saccharomyces cerevisiae
Reign:Eukaryota
TaxID:764101
EC Number:/


Chains:

Chain Name:Percentage of Residues
within binding site
C100 %


Ligand binding site composition:

B-Factor:71.638
Number of residues:23
Including
Standard Amino Acids: 23
Non Standard Amino Acids: 0
Water Molecules: 0
Cofactors:
Metals:

Cavity properties

LigandabilityVolume (Å3)
0.8301542.375

% Hydrophobic% Polar
42.8957.11
According to VolSite

Ligand :
4kq1_3 Structure
HET Code: U5P
Formula: C9H11N2O9P
Molecular weight: 322.165 g/mol
DrugBank ID: -
Buried Surface Area:61.76 %
Polar Surface area: 181.33 Å2
Number of
H-Bond Acceptors: 9
H-Bond Donors: 3
Rings: 2
Aromatic rings: 0
Anionic atoms: 2
Cationic atoms: 0
Rule of Five Violation: 1
Rotatable Bonds: 4

Mass center Coordinates

XYZ
29.113155.644-27.976


Binding mode :
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Binding mode
BioSolveIT Image generated by PoseView
Protein
Binding Site
Ligand
Interaction pattern
hydrophobic (CA)
aromatic (CZ)
hydrogen bond acceptor (O)
hydrogen bond acceptor/donor (OG)
hydrogen bond donor (N)
positively ionized (NZ)
negatively ionized (OD1)
metal (ZN)

Legend:

Represent the protein/ligand binding mode, centered on the ligand
Dashed lines represents hydrogen bonds and metal interactions
Green residue labels for amino acids with hydrophobic contacts (green lines) to the ligand

Image generated using PoseView by BioSolveIT
BioSolveIT


LigandProteinInteraction
AtomAtomResidueDistance
(Å)
Angle (°)Type
O2NH1ARG- 203.25158.91H-Bond
(Protein Donor)
O1PNARG- 3202.96124.54H-Bond
(Protein Donor)
O2PCZARG- 3203.40Ionic
(Protein Cationic)
C1'CE2PHE- 4804.360Hydrophobic
O4NLEU- 4812.86149.02H-Bond
(Protein Donor)
C2'CE2TYR- 4924.020Hydrophobic
C3'CBTYR- 5134.070Hydrophobic
C5'CBTHR- 5144.480Hydrophobic
O2'OE2GLU- 5172.61132.4H-Bond
(Ligand Donor)